Comparison between the genders for the ages and types

Questions

  • What are the differences between the gender for the different combinations of ages and types?
  • Do we observe the same changes as globally?

Loads

Libraries and functions

==========================================================================
*
*  Package WGCNA 1.63 loaded.
*
*    Important note: It appears that your system supports multi-threading,
*    but it is not enabled within WGCNA in R. 
*    To allow multi-threading within WGCNA with all available cores, use 
*
*          allowWGCNAThreads()
*
*    within R. Use disableWGCNAThreads() to disable threading if necessary.
*    Alternatively, set the following environment variable on your system:
*
*          ALLOW_WGCNA_THREADS=<number_of_processors>
*
*    for example 
*
*          ALLOW_WGCNA_THREADS=4
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=4
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================


Allowing multi-threading with up to 4 threads.
preparing gene to GO mapping data...
preparing IC data...
preparing gene to GO mapping data...
preparing IC data...
preparing gene to GO mapping data...
preparing IC data...

Data

Stats

Wald padj < 0.05LFC > 0 (Wald padj < 0.05)LFC < 0 (Wald padj < 0.05)
M VS F (SPF, 8w)246212911171
M VS F (GF, 8w)273014191311
M VS F (SPF, 52w)345917351724
M VS F (GF, 52w)334616891657
M VS F (SPF, 104w) 290 148 142
M VS F (GF, 104w) 95 40 55

Differentially expressed genes

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”

Comparison of the numbers per ages

Differentially expressed genes

DEG into gene co-expression network

  • White: up-regulated
  • Black: down-regulated
Age SPF GF
8w M vs F M vs F
52w M vs F M vs F
104w M vs F M vs F

GO analysis

Biological process

Dot-plot with the most over-represented BP GO (20 most significant p-values for the different comparison)

Network based on description similarity

Age SPF GF
8w M vs F M vs F
52w M vs F M vs F
104w M vs F M vs F

M VS F (SPF, 8w)

scatterplotThree

M VS F (GF, 8w)

scatterplotThree

M VS F (SPF, 52w)

scatterplotThree

M VS F (GF, 52w)

scatterplotThree

M VS F (SPF, 104w)

scatterplotThree

M VS F (GF, 104w)

scatterplotThree

Cellular components

Dot-plot with the most over-represented CC GO (20 most significant p-values for the different comparison)

Molecular functions

Dot-plot with the most over-represented MF GO (20 most significant p-values for the different comparison)

Warning message:
“Removed 6 rows containing missing values (geom_point).”

KEGG pathways

[1] "Note: 17 of 5736 unique input IDs unmapped."
[1] "Note: 17 of 5736 unique input IDs unmapped."

Pathway graphs available at ../results/dge/type-effect/type_gender_age/over_repr_kegg/

[1] "Note: 17 of 5736 unique input IDs unmapped."
Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  C
limit_output extension: Maximum message size of 10000 exceeded with 10040 characters

Pathway graphs available at ../results/dge/type-effect/type_gender_age/under_repr_kegg/